If you have the capability with your setup, the easy way is to just use manual marks. You position the 'laser' dot or blade if you have no light pen capabilities, over each mark in turn. The hard way is to register the media in the printer, print just the marks, place a square of white vinyl of each printed mark, back the media up in the printer to the registration point you used to start this, print your image. I print on a lot of metallic vinyl and am forced by circumstances to use the double print method. Thus this is practical advice from actual experience.
To all those of the 'draw marks on masking tape' school, where, exactly, do you draw the marks?